Display gnomAD allele frequencies in HiGlass
Note: This is the source code for the gnomAD track only! You might want to check out the following repositories as well:
- HiGlass viewer: https://github.com/higlass/higlass
- HiGlass server: https://github.com/higlass/higlass-server
- HiGlass docker: https://github.com/higlass/higlass-docker
Installation
npm install higlass-gnomad
Data preparation
This track uses vcf files as input data. Here is an example of entries that can be consumed by this track:
#CHROM POS ID REF ALT QUAL FILTER INFO
chr21 5030240 rs1185110752 AC A . PASS AC=16;AN=3778;AF=0.00423504;AF_popmax=0.0296296
chr21 5030242 . C T . AC0;AS_VQSR AC=0;AN=3832;AF=0.00000
chr21 5030249 . T C . AC0;AS_VQSR AC=0;AN=4630;AF=0.00000
chr21 5030253 rs1486393480 G T . AS_VQSR AC=1;AN=5170;AF=0.000193424;AF_popmax=0.000426621
chr21 5030262 . C A . AC0;AS_VQSR AC=0;AN=6230;AF=0.00000
chr21 5030275 . A G . AC0;AS_VQSR AC=0;AN=7910;AF=0.00000
Note that AC (allele count),AN (allele number) and AF (allele frequency) is required in the INFO column.
The track can also display GnomAD SV (structural variants) data. The entries in the vcf file have to be in the following form
#CHROM POS ID REF ALT QUAL FILTER INFO
chr3 146453963 nssv16051216 T <INS> . . AC=1;AF=4.6e-05;AN=21694;END=146453963;SVLEN=281;SVTYPE=INS
chr3 146480766 nssv15885393 C <DEL> . . AC=36;AF=0.001659;AN=21694;END=146481132;SVLEN=-367;SVTYPE=DEL
chr3 146485150 nssv15972036 C <DUP> . . AC=2;AF=9.2e-05;AN=21694;END=146513435;SVLEN=28286;SVTYPE=DUP
chr3 146501411 nssv15885394 T <DEL> . . AC=38;AF=0.001779;AN=21358;END=146502039;SVLEN=-629;SVTYPE=DEL
Usage
The live script can be found at:
Client
- Load this track before the HiGlass core script. For example:
<script src="/higlass-gnomad.js"></script>
<script src="hglib.js"></script>
<script>
...
</script>
Options
The following options are available:
{
"uid": "some_uid",
"type": "gnomad",
"options": {
"colorScale": [
// Variant, Insertion, Deletion, Inversion, Duplication
[0.3, 0.3, 0.3, 0.6],
[0.6, 0.6, 0.0, 0.7],
[1, 0.0, 0.0, 0.55],
[0.68, 0.23, 0.87, 0.8],
[0.27, 0.64, 0.09, 0.8]
],
"showMousePosition": false,
"variantHeight": 12, // Height of the rectangles
"maxTileWidth": 2e5 // Determines how far the user can zoom out before data loading stops
},
"data": {
"type": "vcf",
"vcfUrl": "https://url_to_your_vcf/gnomad.vcf.gz",
"tbiUrl": "https://url_to_your_vcf/gnomad.vcf.gz.tbi",
"chromSizesUrl": "https://url_to_your_chromsize_file/chrom.sizes",
},
"width": 768,
"height": 200
}
ECMAScript Modules (ESM)
We also build out ES modules for usage by applications who may need to import or use higlass-gnomad as a component.
Whenever there is a statement such as the following, assuming higlass-gnomad is in your node_modules folder:
import { GnomadTrack } from 'higlass-gnomad';Then GnomadTrack would automatically be imported from the ./es directory (set via package.json's "module" value).
Support
For questions, please either open an issue or ask on the HiGlass Slack channel at http://bit.ly/higlass-slack
Development
Installation
$ git clone https://github.com/higlass/higlass-gnomad.git
$ cd higlass-gnomad
$ npm installIf you have a local copy of higlass, you can then run this command in the higlass-gnomad directory:
npm link higlassCommands
-
Developmental server:
npm start -
Production build:
npm run build
